Research Publications

Genomics Core Facility provides services including Whole-genome and transcriptome sequencing of non-model organisms, Amplicon sequencing for metagenomic studies, Differential expression analysis of mRNA and miRNA, Degradome sequencing, ChIP and RIP sequencing.

RRID

SCR_023645

Research Publications Supported by This Facility

• Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine.
  Ryu EP, Keller CA, Nichols RG, Tran HN, Brocious PR, Harris LR, Koltun WA, Yochum GS, Davenport ER
  bioRxiv. 2026 May 14; (): . pii: 2026.05.13.725025. doi: 10.64898/2026.05.13.725025. 2026 May 14.
• Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts.
  Guha S, Bledsoe RB, Sutherland J, Epstein B, Fry GM, Venugopal V, Sankari S, Gil-Polo A, Levin G, Geddes BA, Young ND, Tiffin P, Burghardt LT
  ISME J. 2026 Jan 14; 20(1): . doi: 10.1093/ismejo/wrag005. .
• Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.
  Akinniyi OT, Sebastian A, Kulkarni S, Albert I, Reese JC
  RNA. 2026 May 18; 32(6): 930-944. doi: 10.1261/rna.080884.125. 2026 May 18.
• ATAD3 megadalton complex in Plasmodium falciparum is essential for mitochondrial and cellular viability.
  Okoye IC, Lamb IM, Cheung YW, Morrisey JM, Sharma M, Kumar R, Dass S, Shukla A, Rell RS, Mather MW, Llinás M, Chang YW, Vaidya AB
  PLoS Pathog. 2026 Jun; 22(6): e1014317. doi: 10.1371/journal.ppat.1014317. 2026 Jun 3.
• Gene expression analysis and proximity labeling reveal post-transcriptional functions of the yeast RNA polymerase II regulator Def1.
  Akinniyi OT, Kulkarni S, Hribal MM, Keller CA, Giardine BM, Reese JC
  J Biol Chem. 2026 Feb; 302(2): 111003. doi: 10.1016/j.jbc.2025.111003. 2025 Dec 5.
• Draft genomes of Salmonella Dublin from North Dakota State University veterinary diagnostic laboratory.
  Kenney SM, Maddock KJ, Ganda E
  Microbiol Resour Announc. 2026 Apr 9; 15(4): e0063625. doi: 10.1128/mra.00636-25. 2026 Mar 4.
• Hi-C calibration by chemically induced chromosomal interactions.
  Li Y, Fischer CWA, Zou F, Du M, Bai L
  EMBO Rep. 2026 May; 27(10): 2549-2558. doi: 10.1038/s44319-026-00772-x. 2026 Apr 14.
• Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements.
  Kulkarni S, Morrissey A, Sebastian A, Akinniyi OT, Keller CA, Albert I, Mahony S, Reese JC
  bioRxiv. 2026 Jan 17; (): . pii: 2026.01.16.699749. doi: 10.64898/2026.01.16.699749. 2026 Jan 17.
• Cellular Snowballing: Cell Adhesion and Migration Drive the Self-Assembly of Cell-Microgel Biohybrid Spheroids.
  Ataie Z, Kheirabadi S, Li C, Risbud A, Sebastian A, Albert I, Zhang S, Sheikhi A
  Adv Sci (Weinh). 2026 May; 13(30): e11302. doi: 10.1002/advs.202511302. 2026 Mar 17.
• Membranes arrest the coarsening of mitochondrial condensates in human cells.
  Aththawala Gedara SVBD, Penna ST, Feric M
  Commun Biol. 2026 Apr 23; 9(1): . doi: 10.1038/s42003-026-10085-3. 2026 Apr 23.
• Trans-species microRNAs from the parasitic plant Cuscuta campestris specifically avoid loading onto self Argonautes.
  Nien YC, Caron CD, Frutos PJ, Veltri FM, Axtell MJ
  Nucleic Acids Res. 2026 Jul 3; 54(13): . doi: 10.1093/nar/gkag700. .
• Coordination of cell organelles to promote metabolon formation.
  Sha Z, Pedley AM, Iles TD, Zhang S, Staub JR, Zhou R, Benkovic SJ
  Proc Natl Acad Sci U S A. 2026 Feb 3; 123(5): e2532504123. doi: 10.1073/pnas.2532504123. 2026 Jan 26.
• CCR4-NOT is required for suppressing pervasive transcription and retrotransposable elements.
  Kulkarni SD, Morrissey A, Sebastian A, Akinniyi OT, Keller CA, Albert I, Mahony S, Reese JC
  J Biol Chem. 2026 Aug; 302(8): 113289. doi: 10.1016/j.jbc.2026.113289. 2026 Jun 23.
• Genome Instability Precedes Viral Integration in Human Papillomavirus-Transformed Tonsillar Keratinocytes.
  Chan K, Tseng C, Milarachi E, Goldrich D, Schneper L, Sheldon K, Aliaga C, Alam S, Chatterjee S, El-Bayoumy K, Meyers C, Goldenberg D, Broach JR
  Mol Cancer Res. 2025 Feb 6; 23(2): 119-127. doi: 10.1158/1541-7786.MCR-24-0604. .
• Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea.
  Locatelli NS, Baums IB
  G3 (Bethesda). 2025 Apr 17; 15(4): . doi: 10.1093/g3journal/jkaf020. .
• Pasteurized Milk Serves as a Passive Surveillance Tool for Highly Pathogenic Avian Influenza Virus in Dairy Cattle.
  Gontu A, Sekhwal MK, Diaz Huemme A, Li L, Kutsaya S, Ling M, Doshi NK, Byukusenge M, Nissly RH
  Viruses. 2025 Sep 28; 17(10): . doi: 10.3390/v17101318. 2025 Sep 28.
• Widespread release of translational repression across Plasmodium's host-to-vector transmission event.
  Rios KT, McGee JP, Sebastian A, Gedara SA, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE
  PLoS Pathog. 2025 Jan; 21(1): e1012823. doi: 10.1371/journal.ppat.1012823. 2025 Jan 8.
• Interferon-γ/Janus Kinase 1/STAT1 Signaling Represses Forkhead Box A1 and Drives a Basal Transcriptional State in Muscle-Invasive Bladder Cancer.
  Lawrence SS, Yamashita H, Shuman L, Raman JD, Joshi M, Yochum GS, Wu XR, Al-Ahmadie HA, Warrick JI, Walter V, DeGraff DJ
  Am J Pathol. 2025 May; 195(5): 1013-1030. doi: 10.1016/j.ajpath.2025.01.013. 2025 Feb 20.
• High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions.
  Ortigas-Vasquez A, Bowen CD, Renner DW, Baigent SJ, Zhang Y, Yao Y, Nair V, Kennedy DA, Szpara ML
  bioRxiv. 2025 Feb 11; (): . pii: 2025.02.10.637388. doi: 10.1101/2025.02.10.637388. 2025 Feb 11.
• Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera).
  Bresnahan ST, Mahony S, Anton K, Harpur B, Grozinger CM
  Genome Biol. 2025 Jun 18; 26(1): 171. doi: 10.1186/s13059-025-03628-0. 2025 Jun 18.
• Leveraging Transcriptional Signatures of Diverse Stressors for Bumble Bee Conservation.
  Quinlan GM, Hines HM, Grozinger CM
  Mol Ecol. 2025 Feb; 34(3): e17626. doi: 10.1111/mec.17626. 2024 Dec 13.
• miRScore: A rapid and precise microRNA validation tool.
  Vanek A, Griffiths-Jones S, Meyers BC, Shahid S, Axtell MJ
  PLoS Comput Biol. 2025 Nov; 21(11): e1013663. doi: 10.1371/journal.pcbi.1013663. 2025 Nov 3.
• High-fidelity long-read sequencing of an avian herpesvirus reveals extensive intrapopulation diversity in tandem repeat regions.
  Ortigas-Vasquez A, Bowen CD, Renner DW, Baigent SJ, Zhang Y, Yao Y, Nair V, Kennedy DA, Szpara ML
  PLoS Pathog. 2025 Aug; 21(8): e1013435. doi: 10.1371/journal.ppat.1013435. 2025 Aug 25.
• Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.
  Sieg J, Zeng H, Pálová H, Smeds L, Mohanty S, Lahnsteiner A, Chiaromonte F, Makova KD
  bioRxiv. 2025 Nov 4; (): . pii: 2025.11.03.686349. doi: 10.1101/2025.11.03.686349. 2025 Nov 4.
• Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene.
  Nichols RG, Davenport ER
  mSystems. 2025 Jan 21; 10(1): e0148024. doi: 10.1128/msystems.01480-24. 2024 Dec 16.
• Auxin-induced depletion of human CCR4-NOT subunits reveals opposing functions of CNOT1 and CNOT4 in mRNA metabolism.
  Kulkarni S, Smith C, Akinniyi OT, Giardine BM, Keller CA, Arnaoutov A, Reese JC
  J Biol Chem. 2025 Dec; 301(12): 110862. doi: 10.1016/j.jbc.2025.110862. 2025 Oct 27.
• Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.
  Akinniyi OT, Sebastian A, Kulkarni S, Albert I, Reese JC
  bioRxiv. 2025 Dec 12; (): . pii: 2025.12.10.693450. doi: 10.64898/2025.12.10.693450. 2025 Dec 12.
• Reduced Susceptibility to Phytophthora in Non-Transgenic Cacao Progeny Through CRISPR-Cas9 Mediated TcNPR3 Mutagenesis.
  Guiltinan MJ, Landherr L, Maximova SN, DelVecchio D, Sebastian A, Albert I
  Plant Biotechnol J. 2026 Feb; 24(2): 442-454. doi: 10.1111/pbi.70365. 2025 Sep 9.
• The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm.
  Akinniyi OT, Sebastian A, Kulkarni S, Hribal MM, Keller CA, Giardine BM, Albert I, Reese JC
  bioRxiv. 2025 Apr 8; (): . pii: 2024.09.16.613278. doi: 10.1101/2024.09.16.613278. 2025 Apr 8.
• The microbiome and volatile organic compounds reflecting the state of decomposition in an indoor environment.
  Cappas VM, Roy R, Davenport ER, Sykes DG
  Sci Justice. 2025 Sep; 65(5): 101302. doi: 10.1016/j.scijus.2025.101302. 2025 Jun 16.
• CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.
  McKinley LN, Bevilacqua PC
  Methods. 2025 Feb; 234(): 120-130. doi: 10.1016/j.ymeth.2024.12.007. 2024 Dec 9.
• Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora.
  Locatelli NS, Kitchen SA, Stankiewicz KH, Osborne CC, Dellaert Z, Elder H, Kamel B, Koch HR, Fogarty ND, Baums IB
  BMC Genomics. 2024 Nov 20; 25(1): 1119. doi: 10.1186/s12864-024-11025-3. 2024 Nov 20.
• Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea.
  Locatelli NS, Baums IB
  bioRxiv. 2024 Aug 22; (): . pii: 2024.08.21.608299. doi: 10.1101/2024.08.21.608299. 2024 Aug 22.
• Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.
  McKinley LN, Meyer MO, Sebastian A, Chang BK, Messina KJ, Albert I, Bevilacqua PC
  Nucleic Acids Res. 2024 Dec 11; 52(22): 14133-14153. doi: 10.1093/nar/gkae908. .
• Global Release of Translational Repression Across Plasmodium's Host-to-Vector Transmission Event.
  Rios KT, McGee JP, Sebastian A, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE
  bioRxiv. 2024 Mar 16; (): . pii: 2024.02.01.577866. doi: 10.1101/2024.02.01.577866. 2024 Mar 16.
• The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L.
  Kulesza E, Thomas P, Prewitt SF, Shalit-Kaneh A, Wafula E, Knollenberg B, Winters N, Esteban E, Pasha A, Provart N, Praul C, Landherr L, dePamphilis C, Maximova SN, Guiltinan MJ
  BMC Plant Biol. 2024 Jun 26; 24(1): 601. doi: 10.1186/s12870-024-05171-9. 2024 Jun 26.
• Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels.
  Pearce DL, Edson JE, Jennelle CS, Walter WD
  Sci Rep. 2024 May 17; 14(1): 11340. doi: 10.1038/s41598-024-56128-9. 2024 May 17.
• Alcohol and fear conditioning produce strain-specific changes in the dorsal hippocampal transcriptome of adolescent C57BL/6J and DBA/2J mice.
  Seemiller LR, Goldberg LR, Sebastian A, Siegel SR, Praul C, Zeid D, Albert I, Beierle J, Bryant CD, Gould TJ
  Alcohol Clin Exp Res (Hoboken). 2024 Nov; 48(11): 2022-2034. doi: 10.1111/acer.15440. 2024 Sep 16.
• Human CCR4-NOT globally regulates gene expression and is a novel silencer of retrotransposon activation.
  Kulkarni S, Morrissey A, Sebastian A, Giardine B, Smith C, Akinniyi OT, Keller CA, Arnaoutov A, Albert I, Mahony S, Reese JC
  bioRxiv. 2024 Nov 25; (): . pii: 2024.09.10.612038. doi: 10.1101/2024.09.10.612038. 2024 Nov 25.
• Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.
  McKinley LN, Meyer MO, Sebastian A, Chang BK, Messina KJ, Albert I, Bevilacqua PC
  bioRxiv. 2024 Jul 11; (): . pii: 2024.07.11.603121. doi: 10.1101/2024.07.11.603121. 2024 Jul 11.